def main():
parser = argparse.ArgumentParser()
parser.add_argument("tool", type=str)
parser.add_argument("job_order", type=str)
parser.add_argument("--conformance-test", action="store_true")
args = parser.parse_args()
print json.dumps(cli.gen_cli(from_url(args.tool), from_url(args.job_order)))
def run_tests(doc_path, tool_key='tool', test_key='tests'):
doc = from_url(doc_path)
tests = doc[test_key]
for test in tests:
tool = test.get(tool_key)
if test_cmd_line(tool, test.get('test_job'), test):
print 'Test %s completed successfully!' % test.get('id')
else:
print 'Test %s completed failed!' % test.get('id')
def test_tmap_mapall():
path = os.path.join(os.path.dirname(__file__), '../examples/tmap.yml')
doc = from_url(path)
tool, job = doc['mapall'], doc['exampleJob']
print(gen_cli(tool, job))
def test_bwa_mem():
path = os.path.join(os.path.dirname(__file__), '../examples/bwa-mem.yml')
doc = from_url(path)
tool, job = doc['tool'], doc['job']
print(gen_cli(tool, job))
def test_tmap_mapall():
path = os.path.join(os.path.dirname(__file__), "../examples/tmap.yml")
doc = from_url(path)
tool, job = doc["mapall"], doc["exampleJob"]
print gen_cli(tool, job)
def test_bwa_mem():
path = os.path.join(os.path.dirname(__file__), "../examples/bwa-mem.yml")
doc = from_url(path)
tool, job = doc["tool"], doc["job"]
print gen_cli(tool, job)
def cmd_line(doc_path, tool_key='tool', job_key='job'):
doc = from_url(doc_path)
tool, job = doc[tool_key], doc[job_key]
return Adapter(tool).cmd_line(job)
def test_tmap_mapall():
path = os.path.join(os.path.dirname(__file__), '../examples/tmap.yml')
doc = from_url(path)
tool, job = doc['mapall'], doc['exampleJob']
print(gen_cli(tool, job))
def test_bwa_mem():
path = os.path.join(os.path.dirname(__file__), '../examples/bwa-mem.yml')
doc = from_url(path)
tool, job = doc['tool'], doc['job']
print(gen_cli(tool, job))
def validate_all():
validate_schema(TOOL_SCHEMA)
validate_schema(META_SCHEMA)
validate_tool(from_url('../examples/bwa-mem.yml')['tool'])
validate_tool(from_url('../examples/tmap.yml')['mapall'])
